

%--------------------------------------------------------------------------
%\documentclass[11]{book}
%\documentclass[12]{book}

%This is the final one for thesis : 12pt, pages open on the right hand side
\documentclass[11pt, a4paper, oneside, onecolumn, openright]{book}
%\documentclass[11pt, a4paper, oneside, onecolumn, openany, draft]{book}
%\documentclass[11pt, a4paper, oneside, onecolumn, openany]{book}
%\documentclass[11pt, a4paper, twoside, onecolumn, openright]{book}

%\usepackage{fancyhdr}
\usepackage{setspace}
\usepackage{epsfig}
\usepackage{multicol}
%\usepackage{gla-thesis}
%\usepackage{makeidx} %use \index{keyword!subspecifics} to include the entries 

%\usepackage[dvips]{graphics}

%new packages Frank has added
\usepackage[printonlyused]{acronym}
\usepackage{paralist}
%\usepackage[pdftex]{hyperref}
% \hypersetup{
%     bookmarks=true,         % show bookmarks bar?
%     unicode=false,          % non-Latin characters in Acrobat’s bookmarks
%     pdftoolbar=true,        % show Acrobat’s toolbar?
%     pdfmenubar=true,        % show Acrobat’s menu?
%     pdffitwindow=true,      % page fit to window when opened
%     pdftitle={My title},    % title
%     pdfauthor={Author},     % author
%     pdfsubject={Subject},   % subject of the document
%     pdfnewwindow=true,      % links in new window
%     pdfkeywords={keywords}, % list of keywords
%     colorlinks=true,       % false: boxed links; true: colored links
%     linkcolor=blue,          % color of internal links
%     citecolor=green,        % color of links to bibliography
%     filecolor=magenta,      % color of file links
%     urlcolor=cyan           % color of external links
%     plainpages=false
% }


%\usepackage{attachfile}
%\usepackage{pdfpages}
%\usepackage[pdftex]{color,graphicx}
%Line spacing - possible 1.5 for final document, 1.2 for now
%\setstretch{1.2}
\setstretch{1.5}

%\pagestyle{fancy}
%\fancyhf{}
%\fancyhead[LE,RO]{\bfseries\thepage}
%\fancyhead[LO]{\bfseries\rightmark}
%\fancyhead[RE]{\bfseries\leftmark}

%\setlength{\parindent}{0cm}
%\setlength{\parskip}{0.25cm}
%\setlength{\parsep}{0.25cm}
% just a little bit of space on top of {verbatim}s
%\setlength{\topsep}{0.1cm}  

\setlength{\oddsidemargin}{1.7cm}
\setlength{\evensidemargin}{-0.8cm}
\setlength{\topmargin}{-0.8cm}
\setlength{\textwidth}{15.4cm}
\setlength{\textheight}{24cm}


%Frank added new bit here
\setcounter{secnumdepth}{4}
%\include{header}

%--------------------------------------------------------------------------
%\bibliographystyle{plain}
%\bibliographystyle{alpha}

%\usepackage{apalike}
%\bibliographystyle{apalike}
	
\bibliographystyle{newPlain}

%\bibliographystyle{amsplain}
%\bibliographystyle{ieeetr}
%\bibliographystyle{siam}
	
%--------------------------------------------------------------------------
% Set up for pdf and hyperref

%Test!!  for diff headings... from http://www.iam.ubc.ca/~newbury/tex/page-set-up.html
\pagestyle{myheadings}    % Go for customized headings
%\begin{singlespace}
\newcommand{\newchap}[1]  %Re-define the chaptering command to use
	{                   % THESE headers.
	\chapter{#1} 
	  \markboth{Chapter \thechapter.  {#1}\hfill \hfill}{Chapter   \thechapter.  {#1}\hfill \hfill}
	}
%\end{singlespace}	
	
%These are headings for the appendices
\newcommand{\chapappend}[1]    %Re-define the chaptering command to use
	{                   % THESE headers.
	\chapter{#1}
	  \markboth{Appendix \thechapter.  {#1}\hfill \hfill}{Appendix \thechapter.  {#1}\hfill \hfill}
	}
%Test


	

\newif\ifpdf
\ifx\pdfoutput\undefined
  \pdffalse  % we are not running pdflatex
\else \pdftrue  % we are running pdflatex
\fi

%\ifpdf
%  \usepackage[pdftex]{hyperref}
%\else
%  \usepackage[hypertex]{hyperref}
%\fi

%\hypersetup{
%  bookmarksopen=true,
%  colorlinks=true}
%\setcounter{tocdepth}{3}
%\setcounter{secnumdepth}{2}

%--------------------------------------------------------------------------
\begin{document}

%--------------------------------------------------------------------------
% Title page
% based on Laszlo's gla-thesis.sty

\begin{titlepage}
\newpage

\begin{center}

\begin{minipage}[t]{6in}
\begin{flushleft}


	%\includegraphics[scale=0.15]{Newcastle_Master_Col.eps}


  %\includegraphics{../Images/university.ps}            % Glasgow University crest
%  \epsfysize=30mm \epsfbox{/users/grad/jonesa/Thesis/Images/university.ps}
\end{flushleft}
\end{minipage}

\begin{minipage}[t]{6in}
\begin{flushright}
\vspace{-1in}
{\large Institute for Cell and Molecular Biosciences\\
		 and the School of Computing Science\\}
\end{flushright}
\end{minipage}

\begin{singlespace}
\vspace{25mm}
{\bf\huge Lab-book for \\* the development of standards for proteomics research \\* and \\* a proteomics investigation of diabetic adipocyte models\\}

\end{singlespace}
 
\vspace{30mm}
{\Huge\sl Frank Gibson}

\vspace{35mm}

\begin{minipage}[t]{4in}
\begin{center}
{\LARGE \textit{Submitted for the degree of Doctor of Philosophy 
  in the Institute for Cell and Molecular Biosciences, Newcastle University}}\\
\vspace{5mm}
{\LARGE September\ 2007}                    % Submission date
\end{center}
\end{minipage}

\vspace{45mm}
%Put back in at end
%\copyright\ 2007, Frank Gibson

\end{center}
\end{titlepage}

%--------------------------------------------------------------------------
% Initial matter

\frontmatter
%\include{Abstract}
%\include{Acknowledge}


\begin{singlespace}
\tableofcontents
%Frank added new bit here
\setcounter{tocdepth}{4}
%
\begin{sloppypar}
\listoffigures
\end{sloppypar}
\listoftables
\include{LabBook-abbrevs}
\end{singlespace}

%--------------------------------------------------------------------------
% Introductory parts

\mainmatter


\include{experiment} 

\include{protocol}
\include{recipie}


%--------------------------------------------------------------------------
% Appendix

\begin{appendix}

%%!! Need to do different headers for the appendix... done?
%\include{AppendixMaterialsandMethods}
%
% 
 \setstretch{1.2}
% \include{AppendixFGE}
% \include{AppendRAPADSql}	
%\include{AppendixDataStandards}
\end{appendix}

%--------------------------------------------------------------------------
% Bibliography

\backmatter

\begin{singlespace}
\pagestyle{plain}
\bibliography{lab-book-library}
\end{singlespace}




\end{document}




